Auto Upgrade Destroyed File Permissions

[The.Reaper]

Okay so i tried to run the auto upgrade on my boards with the most recent upgrade, the updated crashed mid way through and gave me a Server Error 500.

From this point onwards my whole servers chomod permissions were changed as well as strangly my apache2.conf file was wiped, everything had stopped working, i contacted IPB support but they seem to be just giving me small fixes that then lead onto another problem due to the permission changes.

My question is firstly, is there an easy way to fix this issue? If not is there a list of what folders/files need what permissions?

 

Thanks